private void zscoreSinglePlateToolStripMenuItem_Click(object sender, EventArgs e)
{
List<double> Pos = new List<double>();
List<double> Neg = new List<double>();
List<cSimpleSignature> ZFactorList = new List<cSimpleSignature>();
int NumDesc = CompleteScreening.ListDescriptors.Count;
cWell TempWell;
// loop on all the desciptors
for (int Desc = 0; Desc < NumDesc; Desc++)
{
Pos.Clear();
Neg.Clear();
if (CompleteScreening.ListDescriptors[Desc].IsActive() == false) continue;
for (int row = 0; row < CompleteScreening.Rows; row++)
for (int col = 0; col < CompleteScreening.Columns; col++)
{
TempWell = CompleteScreening.GetCurrentDisplayPlate().GetWell(col, row, true);
if (TempWell == null) continue;
else
{
if (TempWell.GetClass() == 0)
Pos.Add(TempWell.ListDescriptors[Desc].GetValue());
if (TempWell.GetClass() == 1)
Neg.Add(TempWell.ListDescriptors[Desc].GetValue());
}
}
if (Pos.Count < 3)
{
MessageBox.Show("No or not enough positive controls !", "Warning", MessageBoxButtons.OK, MessageBoxIcon.Exclamation);
return;
}
if (Neg.Count < 3)
{
MessageBox.Show("No or not enough negative controls !", "Warning", MessageBoxButtons.OK, MessageBoxIcon.Exclamation);
return;
}
double ZScore = 1 - 3 * (std(Pos.ToArray()) + std(Neg.ToArray())) / (Math.Abs(Mean(Pos.ToArray()) - Mean(Neg.ToArray())));
GlobalInfo.ConsoleWriteLine(CompleteScreening.ListDescriptors[Desc].GetName() + ", Z-Score = " + ZScore);
cSimpleSignature TmpDesc = new cSimpleSignature(CompleteScreening.ListDescriptors[Desc].GetName(), ZScore);
ZFactorList.Add(TmpDesc);
}
ZFactorList.Sort(delegate(cSimpleSignature p1, cSimpleSignature p2) { return p1.AverageValue.CompareTo(p2.AverageValue); });
Series CurrentSeries = new Series();
CurrentSeries.ChartType = SeriesChartType.Column;
CurrentSeries.ShadowOffset = 1;
Series SeriesLine = new Series();
SeriesLine.Name = "SeriesLine";
SeriesLine.ShadowOffset = 1;
SeriesLine.ChartType = SeriesChartType.Line;
int RealIdx = 0;
for (int IdxValue = 0; IdxValue < ZFactorList.Count; IdxValue++)
{
if (double.IsNaN(ZFactorList[IdxValue].AverageValue)) continue;
if (double.IsInfinity(ZFactorList[IdxValue].AverageValue)) continue;
CurrentSeries.Points.Add(ZFactorList[IdxValue].AverageValue);
CurrentSeries.Points[RealIdx].Label = string.Format("{0:0.###}", ZFactorList[IdxValue].AverageValue);
CurrentSeries.Points[RealIdx].Font = new Font("Arial", 10);
CurrentSeries.Points[RealIdx].ToolTip = ZFactorList[IdxValue].Name;
CurrentSeries.Points[RealIdx].AxisLabel = ZFactorList[IdxValue].Name;
SeriesLine.Points.Add(ZFactorList[IdxValue].AverageValue);
SeriesLine.Points[RealIdx].BorderColor = Color.Black;
SeriesLine.Points[RealIdx].MarkerStyle = MarkerStyle.Circle;
SeriesLine.Points[RealIdx].MarkerSize = 4;
RealIdx++;
}
SimpleForm NewWindow = new SimpleForm(CompleteScreening);
int thisWidth = 200 * RealIdx;
if (thisWidth > (int)GlobalInfo.OptionsWindow.numericUpDownMaximumWidth.Value) thisWidth = (int)GlobalInfo.OptionsWindow.numericUpDownMaximumWidth.Value;
NewWindow.Width = thisWidth;
NewWindow.Height = 400;
NewWindow.Text = "Z-factors";
ChartArea CurrentChartArea = new ChartArea();
CurrentChartArea.BorderColor = Color.Black;
CurrentChartArea.AxisX.Interval = 1;
NewWindow.chartForSimpleForm.Series.Add(CurrentSeries);
NewWindow.chartForSimpleForm.Series.Add(SeriesLine);
CurrentChartArea.AxisX.IsLabelAutoFit = true;
NewWindow.chartForSimpleForm.ChartAreas.Add(CurrentChartArea);
CurrentChartArea.Axes[1].Maximum = 2;
CurrentChartArea.Axes[1].IsMarksNextToAxis = true;
CurrentChartArea.Axes[0].MajorGrid.Enabled = false;
CurrentChartArea.Axes[1].MajorGrid.Enabled = false;
NewWindow.chartForSimpleForm.TextAntiAliasingQuality = TextAntiAliasingQuality.High;
CurrentChartArea.BackGradientStyle = GradientStyle.TopBottom;
CurrentChartArea.BackColor = CompleteScreening.GlobalInfo.OptionsWindow.panel1.BackColor;
CurrentChartArea.BackSecondaryColor = Color.White;
Title CurrentTitle = new Title(CompleteScreening.GetCurrentDisplayPlate().Name + " Z-factors");
CurrentTitle.Font = new System.Drawing.Font("Arial", 11, FontStyle.Bold);
NewWindow.chartForSimpleForm.Titles.Add(CurrentTitle);
NewWindow.Show();
NewWindow.chartForSimpleForm.Update();
NewWindow.chartForSimpleForm.Show();
NewWindow.Controls.AddRange(new System.Windows.Forms.Control[] { NewWindow.chartForSimpleForm });
}
private SimpleForm BuildSSMD(int Desc)
{
List<double> Pos = new List<double>();
List<double> Neg = new List<double>();
List<cSimpleSignature> ZFactorList = new List<cSimpleSignature>();
cWell TempWell;
int NumberOfPlates = CompleteScreening.ListPlatesActive.Count;
// loop on all the plate
for (int PlateIdx = 0; PlateIdx < NumberOfPlates; PlateIdx++)
{
cPlate CurrentPlateToProcess = CompleteScreening.ListPlatesActive.GetPlate(CompleteScreening.ListPlatesActive[PlateIdx].Name);
Pos.Clear();
Neg.Clear();
for (int row = 0; row < CompleteScreening.Rows; row++)
for (int col = 0; col < CompleteScreening.Columns; col++)
{
TempWell = CurrentPlateToProcess.GetWell(col, row, true);
if (TempWell == null) continue;
else
{
if (TempWell.GetClass() == 0)
Pos.Add(TempWell.ListDescriptors[Desc].GetValue());
if (TempWell.GetClass() == 1)
Neg.Add(TempWell.ListDescriptors[Desc].GetValue());
}
}
double SSMDScore = (Mean(Pos.ToArray()) - Mean(Neg.ToArray())) / Math.Sqrt(std(Pos.ToArray()) * std(Pos.ToArray()) + std(Neg.ToArray()) * std(Neg.ToArray()));
GlobalInfo.ConsoleWriteLine(CurrentPlateToProcess.Name + ", SSMD = " + SSMDScore);
//cDescriptor TmpDesc = new cDescriptor(SSMDScore, CurrentPlateToProcess.Name);
cSimpleSignature TmpDesc = new cSimpleSignature(CurrentPlateToProcess.Name, SSMDScore);
ZFactorList.Add(TmpDesc);
}
Series CurrentSeries = new Series();
CurrentSeries.ChartType = SeriesChartType.Column;
CurrentSeries.ShadowOffset = 1;
Series SeriesLine = new Series();
SeriesLine.Name = "SeriesLine";
SeriesLine.ShadowOffset = 1;
SeriesLine.ChartType = SeriesChartType.Line;
int RealIdx = 0;
for (int IdxValue = 0; IdxValue < ZFactorList.Count; IdxValue++)
{
if (ZFactorList[IdxValue].AverageValue.ToString() == "NaN") continue;
CurrentSeries.Points.Add(ZFactorList[IdxValue].AverageValue);
CurrentSeries.Points[RealIdx].Label = string.Format("{0:0.###}", ZFactorList[IdxValue].AverageValue);
CurrentSeries.Points[RealIdx].Font = new Font("Arial", 10);
CurrentSeries.Points[RealIdx].ToolTip = ZFactorList[IdxValue].Name;
CurrentSeries.Points[RealIdx].AxisLabel = ZFactorList[IdxValue].Name;
SeriesLine.Points.Add(ZFactorList[IdxValue].AverageValue);
SeriesLine.Points[RealIdx].BorderColor = Color.Black;
SeriesLine.Points[RealIdx].MarkerStyle = MarkerStyle.Circle;
SeriesLine.Points[RealIdx].MarkerSize = 4;
RealIdx++;
}
SimpleForm NewWindow = new SimpleForm();
int thisWidth = 200 * RealIdx;
if (thisWidth > (int)GlobalInfo.OptionsWindow.numericUpDownMaximumWidth.Value)
thisWidth = (int)GlobalInfo.OptionsWindow.numericUpDownMaximumWidth.Value;
NewWindow.Width = thisWidth;
NewWindow.Height = 400;
NewWindow.Text = "SSMD";
ChartArea CurrentChartArea = new ChartArea();
CurrentChartArea.BorderColor = Color.Black;
CurrentChartArea.AxisX.Interval = 1;
NewWindow.chartForSimpleForm.Series.Add(CurrentSeries);
NewWindow.chartForSimpleForm.Series.Add(SeriesLine);
CurrentChartArea.AxisX.IsLabelAutoFit = true;
NewWindow.chartForSimpleForm.ChartAreas.Add(CurrentChartArea);
// CurrentChartArea.Axes[1].Maximum = 2;
CurrentChartArea.Axes[1].IsMarksNextToAxis = true;
CurrentChartArea.Axes[0].MajorGrid.Enabled = false;
CurrentChartArea.Axes[1].MajorGrid.Enabled = false;
NewWindow.chartForSimpleForm.TextAntiAliasingQuality = TextAntiAliasingQuality.High;
CurrentChartArea.BackGradientStyle = GradientStyle.TopBottom;
CurrentChartArea.BackColor = CompleteScreening.GlobalInfo.OptionsWindow.panel1.BackColor;
CurrentChartArea.BackSecondaryColor = Color.White;
Title CurrentTitle = new Title(CompleteScreening.ListDescriptors[Desc].GetName() + " SSMD");
CurrentTitle.Font = new System.Drawing.Font("Arial", 11, FontStyle.Bold);
NewWindow.chartForSimpleForm.Titles.Add(CurrentTitle);
return NewWindow;
}
private void buttonRejectPlates_Click(object sender, EventArgs e)
{
if (CompleteScreening == null) return;
List<double> Pos = new List<double>();
List<double> Neg = new List<double>();
List<cSimpleSignature> ZFactorList = new List<cSimpleSignature>();
cWell TempWell;
int Desc = this.comboBoxDescriptorToDisplay.SelectedIndex;
int NumberOfPlates = CompleteScreening.ListPlatesActive.Count;
// loop on all the plate
for (int PlateIdx = 0; PlateIdx < NumberOfPlates; PlateIdx++)
{
cPlate CurrentPlateToProcess = CompleteScreening.ListPlatesActive.GetPlate(CompleteScreening.ListPlatesActive[PlateIdx].Name);
Pos.Clear();
Neg.Clear();
for (int row = 0; row < CompleteScreening.Rows; row++)
for (int col = 0; col < CompleteScreening.Columns; col++)
{
TempWell = CurrentPlateToProcess.GetWell(col, row, true);
if (TempWell == null) continue;
else
{
if (TempWell.GetClass() == comboBoxRejectionPositiveCtrl.SelectedIndex)
Pos.Add(TempWell.ListDescriptors[Desc].GetValue());
if (TempWell.GetClass() == comboBoxRejectionNegativeCtrl.SelectedIndex)
Neg.Add(TempWell.ListDescriptors[Desc].GetValue());
}
}
if (Pos.Count < 3)
{
richTextBoxInformationRejection.AppendText("\nPlate: " + CurrentPlateToProcess.Name + ". No or not enough positive controls !");
continue;
}
if (Neg.Count < 3)
{
richTextBoxInformationRejection.AppendText("\nPlate: " + CurrentPlateToProcess.Name + ". No or not enough negative controls !");
continue;
}
double ZScore = 1 - 3 * (std(Pos.ToArray()) + std(Neg.ToArray())) / (Math.Abs(Mean(Pos.ToArray()) - Mean(Neg.ToArray())));
if (double.IsNaN(ZScore))
{
richTextBoxInformationRejection.AppendText("\nFailed to estimate Z' factor on plate " + CurrentPlateToProcess.Name + " => rejected");
}
cSimpleSignature TmpDesc = new cSimpleSignature(CurrentPlateToProcess.Name, ZScore);
ZFactorList.Add(TmpDesc);
}
int NumDesc = CompleteScreening.ListDescriptors.Count;
int PlateRejected = 0;
richTextBoxInformationRejection.Clear();
richTextBoxInformationRejection.AppendText("\nDescriptor: "+CompleteScreening.ListDescriptors[Desc].GetName()+"\n");
foreach (cSimpleSignature TmpZFactor in ZFactorList)
{
if (TmpZFactor.AverageValue <= (float)numericUpDownRejectionThreshold.Value) PlateRejected++;
}
if (PlateRejected == ZFactorList.Count)
{
MessageBox.Show("By applying such rejection scheme, all the plates would be removed.\n", "Process cancelled !", MessageBoxButtons.OK, MessageBoxIcon.Error);
return;
}
PlateRejected = 0;
foreach (cSimpleSignature TmpZFactor in ZFactorList)
{
richTextBoxInformationRejection.AppendText("\n" + TmpZFactor.Name + ": Z' factor = " + TmpZFactor.AverageValue.ToString("N3"));
if (TmpZFactor.AverageValue <= (float)numericUpDownRejectionThreshold.Value)
{
richTextBoxInformationRejection.AppendText(" <= " + (float)numericUpDownRejectionThreshold.Value + " => rejected!");
CompleteScreening.ListPlatesActive.Remove(CompleteScreening.ListPlatesAvailable.GetPlate(ZFactorList[PlateRejected].Name));
toolStripcomboBoxPlateList.Items.Remove(ZFactorList[PlateRejected].Name);
}
else
{
richTextBoxInformationRejection.AppendText(" > " + (float)numericUpDownRejectionThreshold.Value + " => preserved!");
}
PlateRejected++;
}
RefreshInfoScreeningRichBox();
CompleteScreening.CurrentDisplayPlateIdx = 0;
if(toolStripcomboBoxPlateList.Items.Count>0)
toolStripcomboBoxPlateList.SelectedIndex = 0;
CompleteScreening.GetCurrentDisplayPlate().DisplayDistribution(CompleteScreening.ListDescriptors.CurrentSelectedDescriptor, false);
}